Abstract
Salt tolerance of rice (Oryza sativa L.) at the seed germination stage is one of the major determinants for the stable stand establishment in salinity soil. One population of recombinant inbred lines (RILs, F2:9), derived from a cross between a japonica rice landrace tolerant to salt stress and a sensitive indica rice variety, was used to determine the germination traits including imbibition rate and germination percentage under control (water) and salt stress (100 mM NaCl) for 10 days at 30 °C. The multiple interval mapping (MIM) were applied to conduct QTL for the traits. The results showed that seed germination was a quantitative trait controlled by several genes, and strongly affected by salt stress. A total of 16 QTLs were detected in this study, and each QTL could explain 4.6–43.7% of the total phenotypic variance. The expression of these QTLs might be developmentally regulated and growth stage-specific. In addition, only one digenic interaction was detected under salt stress, showing small effect on germination percentage with R2 2.7%. Among sixteen QTLs detected in this study, four were major QTLs with R2 > 30%, and some novel alleles of salt tolerance genes in rice. The results demonstrated that the japonica rice Jiucaiqing is a good source of gene(s) for salt tolerance and the major or minor QTLs identified could be used to improve the salt tolerance by marker-assisted selection (MAS) in rice.
Similar content being viewed by others
References
Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
Cui H, Peng B, Xing Z, Xu G, Yu B, Zhang Q (2002) Molecular dissection of seedling-vigor and associated physiological traits in rice. Theor Appl Genet 5:745–753
Dellaporta SL, Wood T, Hicks TB (1983) A plant DNA mini preparation: version II. Plant Mol Bio Rep 1:19–21
Flowers TJ, Koyama ML, Flowers SA, Sudhakar C, Singh KP, Yeo AR (2000) QTL: their place in engineering tolerance of rice to salinity. J Exp Bot 51:99–106
Foolad MR, Zhang LP, Subbiah P (2003) Genetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping. Genome 46:536–545
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799
Gu XY, Mei MT, Yan XL, Zheng SL, Lu YG (2000) Preliminary detection of quantitative trait loci for salt tolerance in rice. Chin J Rice Sci 14:65–70
Hayashi E, Aoyama N, Still DW (2008) Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome 51:928–947
Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H (2009) A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor Appl Genet 118:1477–1488
Jiang L, Liu S, Hou M, Tang J, Chen L, Zhai H, Wan J (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Res 98:68–75
Johnson DW, Smith SE, Dobrenz AK (1992) Genetic and phenotypic relationships in response to NaCl at different developmental stages in alfalfa. Theor Appl Genet 83:833–838
Kim ST, Wang Y, Kang SY, Kim SG, Rakwal R, Kim YC, Kang KY (2009) Developing rice embryo proteomics reveals essential role for embryonic proteins in regulation of seed germination. J Proteome Res 8:3598–3605
Koyama ML, Levesley A, Koebner RMD, Flowers TJ, Yeo AR (2001) Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiol 125:406–422
Kubo T, Yoshimura A (2005) Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice (Oryza sativa L.). Theor Appl Genet 110:346–355
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Lee KS, Choi WY, Ko JC, Kim TS, Gregorio GB (2003) Salinity tolerance of japonica and indica rice (Oryza sativa L.) at the seedling stage. Planta 216:1043–1046
Lee SY, Ahn JH, Cha YS, Yun DW, Lee MC, Ko JC, Lee KS, Eun MY (2006) Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cells 21:192–196
Levitt J (1980) Response of pants to environmental stress, 2nd edn. Academic Press, New York
Lin HX, Zhu MZ, Yano MJ, Gao P, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260
Mccormac AC, Keefe PD (1990) Cauliflower (Brassica oleracea L.) seed vigour: imbibition effects. J Exp Bot 41:893–899
McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M, Mori-shima H, Kinoshita T (1997) Report on QTL nomenclature. Rice Genet News 14:11–13
McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 6:199–207
Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G (2009) Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell 21:403–419
Park SJ, Kwak KJ, Oh TR, Kim YO, Kang H (2009) Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol 50:869–878
Prasad SR, Bagali PG, Hittalmani S, Shashidhar HE (2000) Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). Curr Sci 78:162–164
Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146
Sanguinetti CJ, Neto ED, Simpson AJ (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:914–921
Takehisa H, Shimodate T, Fukuta Y, Ueda T, Yano M, Yamaya T, Kameya T, Sato T (2004) Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res 89:85–95
Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712
Vertucci CW, Leopold CA (1987) Water binding in legume seeds. Plant Physiol 85:224–231
Wang JF, Chen HY, Yang QL, Yao MZ, Zhou GA, Zhang HS (2004) Effects of salt concentration and temperature on the screening of salt-tolerance in rice. Chin J Rice Sci 18:449–454
Wang ZF, Wang JF, Bao YM, Wu YY, Su X, Zhang HS (2010a) Inheritance of rice seed germination ability under salt stress. Rice Sci 17:105–110
Wang ZF, Wang JF, Wang FH, Bao YM, Wu YY, Zhang HS (2010b) Segregation analysis of rice seed germination under cold stress using major gene plus polygene mixed inheritance model. Seed Sci Technol 38:104–113
Yano R, Kanno Y, Jikumaru Y, Nakabayashi K, Kamiya Y, Nambara E (2009) CHOTTO1, a putative double APETALA2 repeat transcription factor, is involved in abscisic acid-mediated repression of gibberellin biosynthesis during seed germination in Arabidopsis. Plant Physiol 151:641–654
Yao MZ, Wang JF, Chen HY, Yang QL, Zhou GA, Zhang HS (2004) Genetic analysis of salt tolerance in japonica rice landrace Jiucaiqing from Taihu Lake Region in China. Chin J Rice Sci 18:503–506
Yao MZ, Wang JF, Chen HY, Zhai HQ, Zhang HS (2005) Inheritance and QTL mapping of salt tolerance in rice. Rice Sci 12:25–32
Zhu JK (2001) Plant salt tolerance. Trends Plant Sci 6:66–71
Acknowledgments
This work was supported by the National Science Foundation of China (Grant No. 31000748), the Natural Science Foundation of Jiangsu Province (Grant No. BK2010452), the Science and Technology Innovation Foundation of Nanjing Agricultural University (Grant No. KJ09003), and the Changjiang Scholars and Innovative Research Team in University (PCSIRT). We thank reviewers for the careful reading of the manuscript and constructive comments.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wang, Z., Wang, J., Bao, Y. et al. Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178, 297–307 (2011). https://doi.org/10.1007/s10681-010-0287-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10681-010-0287-8